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Toraya T, Tobimatsu T, Shibata N, Mori K. Reactivating chaperones for coenzyme B 12-dependent diol and glycerol dehydratases and ethanolamine ammonia-lyase. Methods Enzymol 2022; 668:243-284. [PMID: 35589195 DOI: 10.1016/bs.mie.2021.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes tend to undergo mechanism-based inactivation during catalysis or inactivation in the absence of substrate. Such inactivation may be inevitable because they use a highly reactive radical for catalysis, and side reactions of radical intermediates result in the damage of the coenzyme. How do living organisms address such inactivation when enzymes are inactivated by undesirable side reactions? We discovered reactivating factors for radical B12 eliminases. They function as releasing factors for damaged cofactor(s) from enzymes and thus mediate their exchange for intact AdoCbl. Since multiple turnovers and chaperone functions were demonstrated, they were renamed "reactivases" or "reactivating chaperones." They play an essential role in coenzyme recycling as part of the activity-maintaining systems for B12 enzymes. In this chapter, we describe our investigations on reactivating chaperones, including their discovery, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methods that we have developed.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan.
| | - Takamasa Tobimatsu
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, Japan
| | - Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
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Toraya T, Tobimatsu T, Mori K, Yamanishi M, Shibata N. Coenzyme B 12-dependent eliminases: Diol and glycerol dehydratases and ethanolamine ammonia-lyase. Methods Enzymol 2022; 668:181-242. [PMID: 35589194 DOI: 10.1016/bs.mie.2021.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Adenosylcobalamin (AdoCbl) or coenzyme B12-dependent enzymes catalyze intramolecular group-transfer reactions and ribonucleotide reduction in a wide variety of organisms from bacteria to animals. They use a super-reactive primary-carbon radical formed by the homolysis of the coenzyme's Co-C bond for catalysis and thus belong to the larger class of "radical enzymes." For understanding the general mechanisms of radical enzymes, it is of great importance to establish the general mechanism of AdoCbl-dependent catalysis using enzymes that catalyze the simplest reactions-such as diol dehydratase, glycerol dehydratase and ethanolamine ammonia-lyase. These enzymes are often called "eliminases." We have studied AdoCbl and eliminases for more than a half century. Progress has always been driven by the development of new experimental methodologies. In this chapter, we describe our investigations on these enzymes, including their metabolic roles, gene cloning, preparation, characterization, activity assays, and mechanistic studies, that have been conducted using a wide range of biochemical and structural methodologies we have developed.
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Affiliation(s)
- Tetsuo Toraya
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan.
| | - Takamasa Tobimatsu
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Koichi Mori
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Mamoru Yamanishi
- Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Naoki Shibata
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, Japan
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Shibata N, Sueyoshi Y, Higuchi Y, Toraya T. Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12
Catalysis. Angew Chem Int Ed Engl 2018; 57:7830-7835. [DOI: 10.1002/anie.201803591] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Naoki Shibata
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Yui Sueyoshi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Yoshiki Higuchi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology; Graduate School of Natural Science and Technology; Okayama University; Tsushima-naka Okayama 700-8530 Japan
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Shibata N, Sueyoshi Y, Higuchi Y, Toraya T. Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12
Catalysis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Naoki Shibata
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Yui Sueyoshi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Yoshiki Higuchi
- Department of Picobiology/Life Science; Graduate School of Life Science; University of Hyogo; 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
- The RIKEN SPring-8 Center; 1-1-1 Koto Sayo-cho, Sato-gun Hyogo 678-5248 Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology; Graduate School of Natural Science and Technology; Okayama University; Tsushima-naka Okayama 700-8530 Japan
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Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones. Arch Biochem Biophys 2014; 544:40-57. [DOI: 10.1016/j.abb.2013.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 11/04/2013] [Accepted: 11/08/2013] [Indexed: 01/12/2023]
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Shibata N, Higuchi Y, Toraya T. How Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase Deals with Both Enantiomers of 2-Amino-1-propanol as Substrates: Structure-Based Rationalization,,. Biochemistry 2010; 50:591-8. [DOI: 10.1021/bi101696h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN Harima Institute, SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN Harima Institute, SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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Shibata N, Tamagaki H, Ohtsuki S, Hieda N, Akita K, Komori H, Shomura Y, Terawaki SI, Toraya T, Yasuoka N, Higuchi Y. Expression, crystallization and preliminary X-ray crystallographic study of ethanolamine ammonia-lyase from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:709-711. [PMID: 20516606 PMCID: PMC2882776 DOI: 10.1107/s1744309110014478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 04/20/2010] [Indexed: 05/29/2023]
Abstract
Ethanolamine ammonia-lyase (EAL) catalyzes the adenosylcobalamin-dependent conversion of ethanolamine to acetaldehyde and ammonia. The wild-type enzyme shows a very low solubility. N-terminal truncation of the Escherichia coli EAL beta-subunit dramatically increases the solubility of the enzyme without altering its catalytic properties. Two deletion mutants of the enzyme [EAL(betaDelta4-30) and EAL(betaDelta4-43)] have been overexpressed, purified and crystallized using the sitting-drop vapour-diffusion method. Crystals of EAL(betaDelta4-30) and EAL(betaDelta4-43) diffracted to approximately 8.0 and 2.1 A resolution, respectively.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.
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Reaction of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12-dependent ethanolamine ammonia-lyase in frozen aqueous solution from 190 to 217 K. Biophys J 2008; 95:5890-900. [PMID: 18805934 DOI: 10.1529/biophysj.108.138081] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The decay kinetics of the aminoethanol-generated Co(II)-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <10(5) s in frozen aqueous solution from 190 to 217 K. X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy of the disordered samples has been used to continuously monitor the full radical pair EPR spectrum during progress of the decay after temperature step reaction initiation. The decay to a diamagnetic state is complete and no paramagnetic intermediate states are detected. The decay exhibits three kinetic regimes in the measured temperature range, as follows. i), Low temperature range, 190 < or = T < or = 207 K: the decay is biexponential with constant fast (0.57 +/- 0.04) and slow (0.43 +/- 0.04) phase amplitudes. ii), Transition temperature range, 207 < T < 214 K: the amplitude of the slow phase decreases to zero with a compensatory rise in the fast phase amplitude, with increasing temperature. iii), High temperature range, T > or = 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (k(obs,m)) and the fast phase of the biexponential decay (k(obs,f)) adhere to the same linear relation on an lnk versus T(-1) (Arrhenius) plot. Thus, k(obs,m) and k(obs,f) correspond to the same apparent Arrhenius prefactor and activation energy (logA(app,f) (s(-1)) = 13.0, E(a,app,f) = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that k(obs,m) and k(obs,f) represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (k(obs,s)) for 190 < or = T < or = 207 K obeys a different linear Arrhenius relation (logA(app,s) (s(-1)) = 13.9, E(a,app,s) = 16.6 kcal/mol). In the transition temperature range, k(obs,s) displays a super-Arrhenius increase with increasing temperature. The change in E(a,app,s) with temperature and the narrow range over which it occurs suggest an origin in a liquid/glass or dynamical transition. A discontinuity in the activation barrier for the chemical reaction is not expected in the transition temperature range. Therefore, the transition arises from a change in the properties of the protein. We propose that a protein dynamical contribution to the reaction, which is present above the transition temperature, is lost below the transition temperature, owing to an increase in the activation energy barrier for protein motions that are coupled to the reaction. For both the fast and slow phases of the low temperature decay, the dynamical transition in protein motions that are obligatorily coupled to the reaction of the Co(II)-substrate radical pair lies below 190 K.
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Warncke K. Characterization of the product radical structure in the Co(II)-product radical pair state of coenzyme B12-dependent ethanolamine deaminase by using three-pulse 2H ESEEM spectroscopy. Biochemistry 2005; 44:3184-93. [PMID: 15736929 DOI: 10.1021/bi048196t] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular structural features of the product radical in the Co(II)-product radical pair catalytic intermediate state in coenzyme B(12)- (adenosylcobalamin-) dependent ethanolamine deaminase from Salmonella typhimurium have been characterized by using X-band three-pulse electron spin-echo envelope modulation (ESEEM) spectroscopy in the disordered solid state. The Co(II)-product radical pair state was prepared by cryotrapping holoenzyme during steady-state turnover on excess 1,1,2,2-(2)H(4)-aminoethanol or natural abundance, (1)H(4)-aminoethanol. Simulation of the (2)H/(1)H quotient ESEEM (obtained at two microwave frequencies, 8.9 and 10.9 GHz) from the interaction of the unpaired electron localized at C2 of the product radical with nearby (2)H nuclei requires four types of coupled (2)H, which are assigned as follows: (a) a single strongly coupled (effective dipole distance, r(eff) = 2.3 A) (2)H in the C5' methyl group of 5'-deoxyadenosine, (b) two weakly coupled (r(eff) = 4.2 A) (2)H in the C5' methyl group, (c) one (2)H coupling from a beta-(2)H bonded to C1 of the product radical (isotropic hyperfine coupling, A(iso) = 4.7 MHz), and (d) a second type of C1 beta-(2)H coupling (A(iso) = 7.7 MHz). The two beta-(2)H couplings are proposed to arise from two C1-C2 rotamer states of the product radical that are present in approximately equal proportion. A model is presented, in which C5' is positioned at a distance of 3.3 A from C2, which is comparable with the C1-C5' distance in the Co(II)-substrate radical pair intermediate. Therefore, the C5'methyl group remains in close (van der Waals) contact with the substrate and product radical species during the radical rearrangement step of the catalytic cycle, and the C5' center is the sole mediator of radical pair recombination in ethanolamine deaminase.
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Affiliation(s)
- Kurt Warncke
- Department of Physics, N201 Mathematics and Science Center, 400 Dowman Drive, Emory University, Atlanta, Georgia 30322, USA.
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Toraya T. Radical catalysis in coenzyme B12-dependent isomerization (eliminating) reactions. Chem Rev 2003; 103:2095-127. [PMID: 12797825 DOI: 10.1021/cr020428b] [Citation(s) in RCA: 312] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tetsuo Toraya
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-naka, Okayama 700-8530, Japan.
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Bandarian V, Reed GH. Analysis of the electron paramagnetic resonance spectrum of a radical intermediate in the coenzyme B(12)-dependent ethanolamine ammonia-lyase catalyzed reaction of S-2-aminopropanol. Biochemistry 2002; 41:8580-8. [PMID: 12093274 DOI: 10.1021/bi0201217] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of the steady-state radical intermediate in the deamination of S-2-aminopropanol catalyzed by ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium has been probed by electron paramagnetic resonance (EPR) spectroscopy using isotopically labeled forms of the substrate and of the adenosylcobalamin cofactor. Electron spin-spin coupling between the radical, centered on the carbon skeleton of the substrate, and the low-spin Co(2+) in cob(II)alamin (B(12r)) produces a dominant splitting of the EPR signals of both the radical and the Co(2+). Analysis of the exchange and dipole-dipole contributions to the spin-spin coupling indicates that the two paramagnetic centers are separated by approximately 11 A. Experiments with (13)C- and with (2)H-labeled forms of S-2-aminopropanol show that the radical is centered on C1 of the carbon skeleton of the substrate in agreement with an earlier report [Babior, B. M., Moss, T. H., Orme-Johnson, W. H., and Beinert, H., (1974) J. Biol. Chem. 249, 4537-4544]. Experiments with perdeutero-S-2-aminopropanol and [2-(15)N]-perdeutero-S-2-aminopropanol reveal a strong hyperfine splitting from the substrate nitrogen, which indicates that the radical is the initial substrate radical created by abstraction of a hydrogen atom from C1 of S-2-aminopropanol. The strong nitrogen hyperfine splitting further indicates that the amino substituent at C2 is approximately eclipsed with respect to the half-occupied p orbital at C1. Experiments with adenosylcobalamin enriched in (15)N in the dimethylbenzimidazole moiety show that the axial base of the cofactor remains attached to the Co(2+) in a functional steady-state reaction intermediate.
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Affiliation(s)
- Vahe Bandarian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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Eda M, Kamachi T, Yoshizawa K, Toraya T. Theoretical Study on the Mechanism of Catalysis of Coenzyme B12-Dependent Diol Dehydratase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.1469] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Warncke K, Utada AS. Interaction of the substrate radical and the 5'-deoxyadenosine-5'-methyl group in vitamin B(12) coenzyme-dependent ethanolamine deaminase. J Am Chem Soc 2001; 123:8564-72. [PMID: 11525664 DOI: 10.1021/ja003658l] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The distance and relative orientation of the C5' methyl group of 5'-deoxyadenosine and the substrate radical in vitamin B(12) coenzyme-dependent ethanolamine deaminase from Salmonella typhimurium have been characterized by using X-band two-pulse electron spin-echo envelope modulation (ESEEM) spectroscopy in the disordered solid state. The (S)-2-aminopropanol-generated substrate radical catalytic intermediate was prepared by cryotrapping steady-state mixtures of enzyme in which catalytically exchangeable hydrogen sites in the active site had been labeled by previous turnover on (2)H(4)-ethanolamine. Simulation of the time- and frequency-domain ESEEM requires two types of coupled (2)H. The strongly coupled (2)H has an effective dipole distance (r(eff)) of 2.2 A, and isotropic coupling constant (A(iso)) of -0.35 MHz. The weakly coupled (2)H has r(eff) = 3.8 A and A(iso) = 0 MHz. The best (2)H ESEEM time- and frequency-domain simulations are achieved with a model in which the hyperfine couplings arise from one strongly coupled hydrogen site and two equivalent weakly coupled hydrogen sites located on the C5' methyl group of 5'-deoxyadenosine. This model indicates that the unpaired electron on C1 of the substrate radical and C5' are separated by 3.2 A and are thus at closest contact. The close proximity of C1 and C5' indicates that C5' of the 5'-deoxyadenosyl moiety directly mediates radical migration between cobalt in cobalamin and the substrate/product site over a distance of 5-7 A in the active site of ethanolamine deaminase.
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Affiliation(s)
- K Warncke
- Department of Physics, Emory University, 1001 Rollins Research Center, 1510 Clifton Road, Atlanta, GA 30322, USA.
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Warncke K, Schmidt JC, Ke SC. Identification of a Rearranged-Substrate, Product Radical Intermediate and the Contribution of a Product Radical Trap in Vitamin B12 Coenzyme-Dependent Ethanolamine Deaminase Catalysis. J Am Chem Soc 1999. [DOI: 10.1021/ja984005w] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kurt Warncke
- Contribution from the Department of Physics, Emory University, Atlanta, Georgia 30322
| | - Jennifer C. Schmidt
- Contribution from the Department of Physics, Emory University, Atlanta, Georgia 30322
| | - Shyue-Chu Ke
- Contribution from the Department of Physics, Emory University, Atlanta, Georgia 30322
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Bandarian V, Poyner RR, Reed GH. Hydrogen atom exchange between 5'-deoxyadenosine and hydroxyethylhydrazine during the single turnover inactivation of ethanolamine ammonia-lyase. Biochemistry 1999; 38:12403-7. [PMID: 10493808 DOI: 10.1021/bi9906219] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The early steps in the single turnover inactivation of ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium by hydroxyethylhydrazine (HEH) have been probed by rapid-mixing sampling techniques, and the destiny of deuterium atoms, present initially in HEH, has been investigated by mass spectrometry. The inactivation reaction produces acetaldehyde, the hydrazine cation radical, 5'-deoxyadenosine, and cob(II)alamin (B(12r)) in amounts stoichiometric with active sites. Rapid-mix freeze-quench EPR spectroscopy and stopped-flow rapid-scan spectrophotometry revealed that the hydrazine cation radical and B(12r) appeared at a rate of approximately 3 s(-)(1) at 21 degrees C. Analysis of 5'-deoxyadenosine isolated from a reaction mixture prepared in (2)H(2)O did not contain deuterium-a result which demonstrates that solvent-exchangeable sites are not involved in the hydrogen-transfer processes. In contrast, all of the 5'-deoxyadenosine, isolated from inactivation reactions with [1,1,2,2-(2)H(4)]HEH, had acquired at least one (2)H from the labeled inactivator. Significant fractions of the 5'-deoxyadenosine acquired two and three deuteriums. These results indicate that hydrogen abstraction from HEH by a radical derived from the cofactor is reversible. The distribution of 5'-deoxyadenosine with one, two, and three deuteriums incorporated and the absence of unlabeled 5'-deoxyadenosine in the product are consistent with a model in which there is direct transfer of hydrogens between the inactivator and the 5'-methyl of 5'-deoxyadenosine. These results reinforce the concept that the 5'-deoxyadenosyl radical is the species that abstracts hydrogen atoms from the substrate in EAL.
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Affiliation(s)
- V Bandarian
- Institute for Enzyme Research, Graduate School, Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison 53705, USA
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Chen E, Chance MR. Nanosecond transient absorption spectroscopy of coenzyme B12. Quantum yields and spectral dynamics. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38257-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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The mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. Evidence that the hydrogen transfer mechanism involves a second intermediate hydrogen carrier in addition to the cofactor. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)36210-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Gani D, Wallis OC, Young DW. Stereochemistry of the rearrangement of 2-aminoethanol by ethanolamine ammonia-lyase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1983; 136:303-11. [PMID: 6628383 DOI: 10.1111/j.1432-1033.1983.tb07742.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
(1R)-2-Amino[1-2H1]ethanol and (1S,2RS)-2-amino[1,2-2H2]ethanols have been synthesised by decarboxylation of (2S,3R)-[3-2H1]serine and (2S,3S)-[2,3-2H2]serine respectively. The stereochemical integrity of these labelled 2-aminoethanols has been ascertained from the 1H-NMR spectra of their N,O-dicamphanoyl derivatives. This assay has also been used to confirm that samples of (2R)- and (2S)-2-amino [2-2H1]ethanols prepared from (2R)- and (2S)-[2-2H1]glycines are stereochemically pure. Ethanolamine ammonia-lyase rearranges (1R)-2-amino[1-2H1]ethanol to acetaldehyde at approximately the same rate as it rearranges unlabelled 2-aminoethanol, whilst (1S,2RS)-2-amino[1,2-2H2]ethanol is rearranged at the same rate as the (1,1-2H2)-labelled substrate. The isotope effect is approximately kH/k2H = 8. The 2H-NMR spectra of the 3,5-dinitrobenzoates of the ethanol produced by reduction in situ of the acetaldehyde formed in the rearrangements show that the 1-2H1 label migrates in (1S,2RS)-2-amino-[1,2-2H2]ethanol and 2-amino[1,1-2H2]ethanol but not in (1R)-2-amino[1-2H1]ethanol. The above results indicate that the adenosylcobalamin-dependent ethanolamine ammonia-lyase catalyses the rearrangement of 2-aminoethanol with migration of the 1-pro-S-hydrogen atom.
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Interaction of N-substituted ethanolamine analogs with ethanolamine ammonia-lyase, an adenosylcobalamin-requiring enzyme. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34691-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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The mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. Studies with isopropanolamine, a true substrate. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(20)79723-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Diziol P, Haas H, Rétey J, Graves SW, Babior BM. The substrate-dependent steric course of the ethanolamine ammonia-lyase reaction. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 106:211-24. [PMID: 7341225 DOI: 10.1111/j.1432-1033.1980.tb06012.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Krouwer JS, Holmquist B, Kipnes RS, Babior BM. The mechanisms of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. Evidence that carbon-cobalt bond cleavage is driven in part by conformational alterations of the corrin ring. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 612:153-9. [PMID: 7362829 DOI: 10.1016/0005-2744(80)90288-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Previous work has shown that the interaction between ethanolamine ammonia-lyase (ethanolamine ammonia-lyase, EC 4.3.1.7) and adenosylcobalamin weakens the C-Co bond of the cofactor with respect to homolytic cleavage. To obtain information concerning the mechanism by which this is accomplished, a study was conducted in which optical and circular dichroism spectroscopy were used to explore the interaction between ethanoloamine ammonia-lyase and a series of adenosylcobalamin analogs composed of an adenyl residue attached to the cobalt atom of cobalamin by a methylene chain whose length varies from 2 to 6 carbons. These studies indicated that the binding of a cobalamin to the active site activates forces which tend to alter the conformation of the enzyme, and with it that of the corrin ring, but that these conformational changes are blocked by bulky Co-beta substituents which restrict corrin ring flexibility. We postulate that at least one element of the force which weakens the C-Co bond of the enzyme-bound cofactor is the relief of conformational strain which occurs when C-Co bond cleavage, by releasing the interfering adenosyl group, permits the enzyme and the corrin ring to assume the energetically favored conformation.
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Babior BM, Krouwer JS. The mechanism of adenosylcobalamin-dependent reactions. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1979; 6:35-102. [PMID: 222536 DOI: 10.3109/10409237909105424] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kamel MY, Maksoud SA. Co-Factor Requirements and Factors Affecting L-Histidine Ammonia-Lease Activity in Vicia faba. ACTA ACUST UNITED AC 1978. [DOI: 10.1016/s0044-328x(78)80247-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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The mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. Reaction of the enzyme.cofactor complex with 2-aminoacetaldehyde. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38108-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Hollaway MR, White HA, Joblin KN, Johnson AW, Lappert MF, Wallis OC. A spectrophotometric rapid kinetic study of reactions catalysed by coenzyme-B12-dependent ethanolamine ammonia-lyase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 82:143-54. [PMID: 620668 DOI: 10.1111/j.1432-1033.1978.tb12005.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. Interaction between the enzyme and a postulated organocobalamin intermediate. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40152-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Abstract
Adenosylcobalamin-dependent rearrangements are enzyme catalyzed reactions in which a hydrogen atom is transfered from one carbon atom to an adjacent one in exchange for a group X which migrates in the opposite direction. In the hydrogen transfer step, the mechanism of which is reasonably well understood, the cofactor serves as an intermediate hydrogen carrier. The transfer of hydrogen to the cofactor involves homolysis of the carbon-cobalt bond to generate cob(II) alamin and the 5'-deoxyadenos-5'-yl radical, followed by abstraction of a hydrogen atom from the substrate to form 5'-deoxyadenosine and the substrate radical. After migration of group X, the hydrogen atom is returned to the product radical by the reverse of the above reactions to generate the final product and reconstitute the cofactor. In contrast to the transfer of hydrogen, the mechanism of group X migration is poorly understood. Many reactions mechanisms have been proposed on chemical grounds, but there is insufficient biochemical evidence to permit a choice among these propsals. A quantity of negative evidence has accumulated suggesting that group X migration does not involve alkylation of the cobalt of cobalamin by the substrate, but in the absence of firm data supporting an alternative mechanism, even this weak conclusion must be regarded as provisional.
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Coenzymes—Nature's Special Reagents. Biochemistry 1977. [DOI: 10.1016/b978-0-12-492550-2.50013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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The mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. The source of the third methyl hydrogen in the 5'-deoxyadenosine generated from the cofactor during catalysis. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33405-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Toraya T, Shirakashi T, Kosuga T, Fukui S. Substrate specificity of coenzyme B12-dependent diol dehydrase: glycerol as both a good substrate and a potent inactivator. Biochem Biophys Res Commun 1976; 69:475-80. [PMID: 1267798 DOI: 10.1016/0006-291x(76)90546-5] [Citation(s) in RCA: 113] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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